Japan Reference - Practical : Transportation inside Japan
- check out the different train pass that you can use.
if you like to visit temples, Kyoto is the best, lots and lots of them there.
Other places also that you might want to check out is Hakone, there is a place there called the ninja trail, which were the actual trail used before.
then there is ninja village in Chiba ( i think ) and in Iga-Ueno in Mie -ken.
In Iga-Ueno, you can actually dress-up like a ninja and walk thru the city in ninja costume
Himeji Castle in Himeji is rated as the most beautiful castle all over Japan.